Compression/decompression method and apparatus for genomic variant call data

Methods and apparatus for compressing and decompressing genetic information from an individual are disclosed. In one arrangement, a data compression method generates a compressed representation of at least a portion of an individual's genome. The method comprises receiving an input file comprising a representation of the at least a portion of the individual's genome in the form of a sequence of variants defined relative to a reference genome. A reference database comprising a plurality of reference lists of genetic variants from other individuals is accessed. Each reference list comprises a sequence of genetic variants from a single, phased haplotype. Two mosaics of segments from the reference lists are identified which match the at least a portion of the individual's genome to within a threshold accuracy. Each mosaic represents a single one of the two haplotypes of the individual's genome in the at least a portion of the individual's genome for which the compressed representation is to be generated. Each of the segments comprises a portion of the sequence of genetic variants from one of the reference lists. The compressed representation is generated by encoding the two mosaics and deviations from the two mosaics.